Genomic Location: Sc0000001:74392...88840
NR annotation: XP_020608898.1, CCR4-NOT transcription complex subunit 4-like isoform X1 [Orbicella faveolata]
Species Galaxea fascicularis · all data for this species · gene families
| CDS |
| gfas1.m1.71.m1 |
| Transcript |
| gfas1.m1.71.m1 |
| Protein |
| gfas1.m1.71.m1 |
| UniProt accession | Description |
|---|---|
| O95628 | CCR4-NOT transcription complex subunit 4 OS=Homo sapiens OX=9606 GN=CNOT4 PE=1 SV=3 |
| Q8BT14 | CCR4-NOT transcription complex subunit 4 OS=Mus musculus OX=10090 GN=Cnot4 PE=1 SV=2 |
| Q09818 | Putative general negative regulator of transcription C16C9.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC16C9.04c PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0003288 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00076 all species → | RRM_1 | RNA recognition motif | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR000571 all species → | Domain | Zinc finger, CCCH-type | Interproscan |
| IPR035979 all species → | Homologous_superfamily | RNA-binding domain superfamily | Interproscan |
| IPR000504 all species → | Domain | RNA recognition motif domain | Interproscan |
| IPR039780 all species → | Family | CCR4-NOT transcription complex subunit 4 | Interproscan |
| IPR012677 all species → | Homologous_superfamily | Nucleotide-binding alpha-beta plait domain superfamily | Interproscan |
| IPR034261 all species → | Domain | CNOT4, RNA recognition motif | Interproscan |
| IPR003954 all species → | Domain | RNA recognition motif domain, eukaryote | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR12603 all species → | CCR4-NOT TRANSCRIPTION COMPLEX RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0046872 all species → | Molecular Function | metal ion binding | Interproscan |
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0004842 all species → | Molecular Function | ubiquitin-protein transferase activity | Interproscan |
| GO:0016567 all species → | Biological Process | protein ubiquitination | Interproscan |
| GO:0030014 all species → | Cellular Component | CCR4-NOT complex | Interproscan |
gfas1.m1.71.m1.Transcript abundance of gfas1.m1.71.m1 across 22 RNA-seq samples of Galaxea fascicularis. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| coral holosome · Control | 7 | 5 | 25.18 | 51.78 | |
| coral holosome · 30ic treatment | 6 | 4 | 27.31 | 44.77 | |
| coral holosome · Prometryn (herbicidess) treatment | 5 | 3 | 33.64 | 86.07 | |
| coral holosome · Prometryn (herbicidess) and 30ic treatment | 4 | 4 | 44.85 | 51.32 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR27118480 | coral holosome · Control | coral holosome | not recorded | Control | SRP476288 | 51.78 |
| SRR27118487 | coral holosome · Control | coral holosome | not recorded | Control | SRP476288 | 38.58 |
| SRR27118486 | coral holosome · Control | coral holosome | not recorded | Control | SRP476288 | 38.53 |
| SRR27118491 | coral holosome · Control | coral holosome | not recorded | Control | SRP476288 | 23.80 |
| SRR27118492 | coral holosome · Control | coral holosome | not recorded | Control | SRP476288 | 23.56 |
| SRR27118485 | coral holosome · Control | coral holosome | not recorded | Control | SRP476288 | 0.00 |
| SRR27118488 | coral holosome · Control | coral holosome | not recorded | Control | SRP476288 | 0.00 |
| SRR27118478 | coral holosome · 30ic treatment | coral holosome | not recorded | 30ic treatment | SRP476288 | 44.77 |
| SRR27118476 | coral holosome · 30ic treatment | coral holosome | not recorded | 30ic treatment | SRP476288 | 41.76 |
| SRR27118479 | coral holosome · 30ic treatment | coral holosome | not recorded | 30ic treatment | SRP476288 | 38.66 |
| SRR27118466 | coral holosome · 30ic treatment | coral holosome | not recorded | 30ic treatment | SRP476288 | 38.66 |
| SRR27118468 | coral holosome · 30ic treatment | coral holosome | not recorded | 30ic treatment | SRP476288 | 0.00 |
| SRR27118477 | coral holosome · 30ic treatment | coral holosome | not recorded | 30ic treatment | SRP476288 | 0.00 |
| SRR27118483 | coral holosome · Prometryn (herbicidess) treatment | coral holosome | not recorded | Prometryn (herbicidess) treatment | SRP476288 | 86.07 |
| SRR27118469 | coral holosome · Prometryn (herbicidess) treatment | coral holosome | not recorded | Prometryn (herbicidess) treatment | SRP476288 | 41.47 |
| SRR27118481 | coral holosome · Prometryn (herbicidess) treatment | coral holosome | not recorded | Prometryn (herbicidess) treatment | SRP476288 | 40.67 |
| SRR27118482 | coral holosome · Prometryn (herbicidess) treatment | coral holosome | not recorded | Prometryn (herbicidess) treatment | SRP476288 | 0.00 |
| SRR27118484 | coral holosome · Prometryn (herbicidess) treatment | coral holosome | not recorded | Prometryn (herbicidess) treatment | SRP476288 | 0.00 |
| SRR27118475 | coral holosome · Prometryn (herbicidess) and 30ic treatment | coral holosome | not recorded | Prometryn (herbicidess) and 30ic treatment | SRP476288 | 51.32 |
| SRR27118489 | coral holosome · Prometryn (herbicidess) and 30ic treatment | coral holosome | not recorded | Prometryn (herbicidess) and 30ic treatment | SRP476288 | 47.57 |
| SRR27118472 | coral holosome · Prometryn (herbicidess) and 30ic treatment | coral holosome | not recorded | Prometryn (herbicidess) and 30ic treatment | SRP476288 | 45.36 |
| SRR27118490 | coral holosome · Prometryn (herbicidess) and 30ic treatment | coral holosome | not recorded | Prometryn (herbicidess) and 30ic treatment | SRP476288 | 35.17 |
Source: CnidoSite RNA-seq expression matrices (GFASC_TPM,
StringTie quantification over 22 runs), joined to SRA sample
metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped
by the descriptor carried in the expression matrix itself.
Genes whose expression across the transcriptome samples of Galaxea fascicularis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.
| Direction | Partners | Most correlated partner | PCC |
|---|---|---|---|
| Positively correlated | 36 | gfas1.m1.6115.m1 | 0.926796259949481 |
| Negatively correlated | 12 | gfas1.m1.16385.m1 | -0.807346933167766 |
Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.
Whether this gene can be visualised in the single-cell atlases of Galaxea fascicularis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.
No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.
Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.
No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.
Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.
| Analysis | What it does | Status | |
|---|---|---|---|
| Primer design | Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed. | template found | open → |
| BLAST | Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start. | template found | open → |
| Expression heatmap | Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it. | ready | open → |
| Gene family / orthogroup | Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue. | open → | |
| Gene set analysis | Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it. | open → |
